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Introduction:
This is not exactly a full game, more like a series of concepts I would like to see, in the same setting. I've divided this post into parts, because it is probably going to be a darn long post. Also:
THIS IS PURELY THEORETICALAlso, I have ideas from other games and will try my best to mention who inspired me
Since it's a long post, feel free to read that of it that sparks your interest and comment on whatever part you want to.
Background:
I think it is in order to mention the background of this idea. I first got it some years ago, when I heard of Bioshock. The person who told me about it failed to mention what type of gameplay it had; just that is was a game where you changed your biological construct to make you stronger and gain new abilities. I had just started playing WoW, and I immediately put the idea into that context. Also, I thought "Science!"
Anyway, I was thrilled about finally getting a better explanation for strength than "Sword of Doom" or simply "Magic". It turned out, though, that Bioshock both was an FPS and featured "magic" (great game nonetheless though). As I started to try my way with programming, 3D art and game design, the idea resurfaced, and over the last year or so, I've kept thinking about it. Now, I'm finally writing it down.
The Setting:
The game is a 3rd-person Sci-fi RPG (ideally with multiplayer), and is set in a dystopian future. I imagined the world to be something along the lines of Fallout 3, but I'm tired of the whole "nuclear annihilation" idea - it smells too much like the 80's. An alternative could be a more Matrix inspired world, where overexpansion has ravaged the world, and resources are scarce. Various environmental and humanitarian disasters have limited humans to a few million inhabitants worldwide. Also, I was thinking about setting most of the game underground, both to limit the size naturally, and to create a unique feel. The explanation for this could be that the ozone-layer has almost completely vanished, and the amount of UV radiation hitting the surface of the world is life threatening to practically any life-form. Also, there will be robots/cyborgs(more on those later), but NO aliens. Well, at least not humanoid/intelligent aliens. The setting would explain why no life form or artificial intelligence has completely taken over. Everyone is basically fighting to survive and scavenge what resources are left.
The Factions:Gene Cult:
Basically, this is where my idea started. The Gene Cult are scientists in a Rapture-ish way; madmen with no regard for ethics (or even human life), hell-bent on "improving" mankind to reach its full potential. They've made a lot of progress, and possess the knowledge to improve and change the human body to add to its abilities. They have different specialties, and are often inspired by animals - adding fangs, poison, additional limbs etc.
Machine Society:
This faction is somewhat of a newer idea since I thought: "if different entities with artificial intelligence were truly created, why would they get along, if humans can't?". (Scientists have already made robots that betray each other http://www.popsci.com/scitech/article/2009-08/evolving-robots-learn-lie-hide-resources-each-other). Since resources are so scarce, the robots would more likely act like humans, thereby creating an actual machine society. It would also raise some interesting philosophical questions, with the birth of the machine and its place in the world.
Human Alliance (optional):
This is basically a "Space Marines" mixed with S.T.A.L.K.E.R. type of human army, with strict military and religious control. Not very original, but they could implement some interesting gameplay devices. For an example, you could have a commander whose squad increases as he gains strength/respect (sort of like Geomancer in DotA multiplies). I made these optional because they are somewhat unoriginal, and not my favourites. Furthermore, a three-faction system isn't necessarily a good idea.
The Alternatives to Items/Gear:
One of the thing that has always bugged me about RPGs are "items/gear" and their link to magic. I honestly do not see how "Wizards Hat" makes you smarter. Also, how exactly does "belt of giant strength" make you stronger? My alternative to this (and one of the main points of this game) is:
You actually change and evolve your character
To elaborate, the first and second faction actually change your character in a physical way that when boiled down is basically the same. If you're part of the Gene Cult, you can for an example create glands that spit chemicals, which when in contact with each other will combust, creating a fire/napalm-breath. Also, you could create wings, stronger legs, camouflage etc. each giving you additional abilities, or improving existing.
As a Cyborg, you would "build" yourself in a similar manner, giving you cloaking, automatic weapons etc. There would of course be ways to limit this, so everyone isn't just the Juggernaut.
When designing the Gene Cult I was looking to nature. Why aren't there dinosaurs anymore if they were so awesome? Simple; it isn't necessarily good to be big. Sure, a Tyrannosaurus Rex can kick some butt in combat, but it is impossible to sneak onto people when you're that big and visible, and it's also hard to catch onto them if they run. Also, the larger an animal is, the higher the blood pressure is (to name one thing), giving it an exploitable weakness. But why not just give yourself camouflage, then? By implementing a system of senses, you avoid "Tauren Rogues". For an example, in Crysis every sound shows up on the mini map. Making the sound as you walk proportional with your weight, you eliminate a giant's ability to ever sneak up on people. Also, heat-vision could counter camouflage, where cold-blooded could counter heat-vision - a system of weaknesses and strengths. Some class archetypes could be:
Brute/warrior:
An ogre type "juggernaut" which is easy to play and packs a punch that's hard to ignore. Lacks some mobility, but can counter with good reflexes, and ability to grab people charging them. They have a lot of room for "weapons" such as fire breath, chemical launchers and other stuff to shoot at people. Also, their survivability is to admire.
Hunter/rogue:
The archetypal stealth-douchebag, which makes up for lack of strength with observational and deceptive abilities. Camouflage, poison, strong hind-legs and a Mantis-style claw could be in their arsenal, along with improved/added senses of different sorts. They get to choose their battles, but in a fair fight aren't worth much. They are also great at immobilizing their enemy and exploiting the situation.
The Hive Mind:
A big and vulnerable entity with an army of creep at their command. They have different biochemical weapons to protect themselves, but use must of their body's strength to command their minions at people. There could be lots of different creatures at your disposal, and you would be able to design an army.
When I got to Machine Society the answer was straight forward: energy. The bigger your machine is, the more power you would need to keep it running. The more power you need the bigger and more cumbersome your engine will be, thereby reducing your mobility. The idea is that a small diesel-ish or electrical engine could support a recon-type cyborg, which is very mobile and has jamming/immobilizing abilities to make up for lack of strength. If people have a weak spot, you don't have to be strong to exploit it. My friend told me that Eve Online has a similar system. Some character archetypes could be:
Battle Droid/Tank:
Engine Type: Hydrogen cells/giant petrol engine - Something that produces a lot of power, while remaining mobile.
Superior firepower sums this one up best. It is fairly cumbersome, but has a lot of energy to direct at weapons. It has a shooter style, and relies on taking out enemies before they get to melee. They are giant bi- or quadrupeds, with guns to blow you apart.
Recon Droid/Mobility Droid:
Engine Type: Diesel/fuel cells/electrical engine - something that sacrifices energy to reduce weight, making the droid extremely mobile.
It would have to rely on precision instead of firepower, taking their enemies by surprise before they can protect themselves. They are slim and slick mechas, perhaps with rocket boosters to give them the edge.
Controller:
Engine Type: Nuclear Reactor - Extremely cumbersome, but gives the amount of energy to control several minions and/or great weapons. (Please note that wireless transfer of energy is possible, making it obsolete to give each machine an engine http://www.ted.com/talks/lang/eng/eric_giler_demos_wireless_electricity.html)
They would of course be controllers of an army of specialized droids, kind of like a Necromancer from Diablo. Their huge weight would make them very immobile in battle, and vulnerable to fast enemies. They would resemble a tank more than a mecha, and have belts instead of wheels. There would be a "travel mode" to make them less annoying to play of course. These would be the equivalent of a magician in fantasy games, and abilities like telekinesis could be obtained with a swarm of small remote controlled robots and wireless electricity.
These archetypes are just examples of characters you would be able to create, because in theory, you can make any selection of abilities. You are, however, limited by how much power you have as a machine, and something similar as Gene Cult (Adam?). Also, you have to sacrifice something to gain something else. Stealth is useless, for an example, if the ground trembles when you walk because of your size. Poison fangs are useless if you can't get close to your enemy. A combination of an immobile brute and a wide angle flamethrower would be quite nice though.
Some Gameplay Mechanics:
Another thing I didn't like about WoW is the targeting system and "name-over-your-head", which makes regular sneaking impossible. It does, however, make the game easier to play, and more intuitive. What I envision is a system that combines the reliance on perception and skill from shooters with some amount of auto-aim on some skills. That makes it easier to react in combat, and avoids the situation where you leap straight into a wall, because your aim or target moved.
It makes combat more complicated, but also gives a great stealth aspect to the game. You would for an example be able to actually hide and ambush people, without the need to make yourself "invisible". Skills like partly transparency would suddenly make sense, as they do in reality.
I envision combat as being heavily reliant on Newtonian physics. Your engine or body parts can muster a certain force, and the force behind your strikes/jumps/movement will be reliant on this. If a light character can muster the same thrust as a heavy character, the light character will of course move faster or jump higher. Weight has a lot to say. It is also harder to knock over 4 tons of badass than 100kg of backstabber. Every character has weak spots, and a light character will typically try to exploit this. A brute can have a thick hide on his back, making it impossible to poke a poisonous claw through, but on the throat the skin is softer. A light droid would have very little armor, and a single blow from a juggernaut will damage it severely. Dodging is very important.
Conclusion:
These ideas are things I've thought about, and gameplay elements I've enjoyed in other games. The main focus of this idea is around realism in the face of Sci-Fi, and giving a credible explanation to the supernatural elements of the game (I am kind of a science geek). Also the focus in combat is to create a system of strengths and weaknesses like nature, without cutting the skill cap too much. The opportunities are endless in this setting, so long as you can explain them, and I think it would be a nice gush of fresh air to see the effect of upgrades on your character instead of on arbitrary stats. If you've made it this far I hope you would like to comment on my ideas. Bear in mind, though, that I only outlined the universe I envisioned, and everything is subject to change.

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A suggestion of limiting factors for the robots. Some things, especially powerful things could not only consume large amounts of power, but also be delicate. Just because its the future doesn't mean everything is made of indestructible ultimate metal.

For instance, we currently have a cloaking technology in its infancy. it works on narrow bands of radiation, like part of the infrared or radio wave spectrum, not all the way across full visible color. None the less, in the future maybe it works on all light from radio up to x-ray. Like today's prototype though, it may rely on a nano-scale surface pattern that literally steers light around the object. Nano-scale surface pattern? That sounds pretty delicate to me!

The biological changes would also bring new dietary needs. You can't make those special flame throwing chemicals without eating the right foods. Not to mention all these new glands and things probably require a lot more energy so you have to eat a lot more overall.

Watch out with the ozone excuse though, if you can evolve whatever you want, there is no reason not to become immune to the extra UV.

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Watch out with the ozone excuse though, if you can evolve whatever you want, there is no reason not to become immune to the extra UV.

You make a good point. Machines would probably have no problem with UV anyway. I was mostly trying to come up with a good excuse to set the game in caves to create some great ambush-opportunities and such.

About the whole 'delicacy', I imagined Hive Minds and Controllers to be delicate to make up for their firepower, but I kinda like the idea of lower reliability on more advanced stuff. It would make sense, since in this future, technology is far from perfect. The invisibility would also only affect certain spectra, but could possibly be improved at a cost. The other senses would still be a problem for the stealthy though.

Edit: Oh, and the dietary needs would make a lot of sense too, I'm just a little worried about people having to run around for food all the time. It would fit into the whole scavenging concept though.

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Being in the Gene Cult sounds fun. I'd say, don't characterize them universally as madmen totally lacking ethics, every group contains people who have a variety of different motivations and moralities. There are a lot of humanitarian reasons why someone might want to introduce genetic changes to a population. For instance I've read 2 or 3 sci-fi novels where humans are given a plant-like outer skin, so no one needs to eat any more, and this ending world hunger.

I think the important part here is, don't think in classes. Start the player as a human then repeatedly give them the choice to become more gene-modded or mechanized or improve as a human as a reward for completing some challenge or quest. Customizing your character is the fun part, make it part of the gameplay, don't waste it on the character creation phase.

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The classes and factions were mostly to simplify the idea, but the main point of the whole "evolution" system is to be able to customize your abilities, so archetypes are achievable (and would probably be favorable in a lot of situations since nature favors specialization), but theoretically you can combine agility with a huge gun, leaving no power left for other things, creating a glass-cannon.

Actually a thing I accidentally left out of my original post was the possibility to betray your faction and combine Biotech and Mechatech. This could definately create some awesome combinations, but since machines and the Gene Cult hate each other, you would have to prove your loyalty to the new faction.

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sunandshadow makes an excellent point. If you look at the mechs as cyborgs and not robots, then they start as totally human same as the gene modders so you should let the player do as he will in both camps. In the spirit of that, instead of having very defined factions you can simply have personal philosophies for specific characters and so most people form opinions on you based on your actions but its on an individual basis.

If you want to have the surface uninhabitable just come up with a bunch of excuses instead. No Ozone is good, man made pollution is good, huge storms, and that only dealing with the possible. Also, you don't need to make it impossible to live on the surface, just significantly more comfortable to live underground. For instance if food is an issue, maybe very little grows on the surface, even with gene modding so its easier to just live near the food. Maybe the surface is very harsh so its possible to go there but living up there is just too much of a bother.